PKR Senses Nuclear and Mitochondrial Signals by Interacting with Endogenous Double-Stranded RNAs

Abstract

Protein kinase RNA-activated (PKR) induces immune response by sensing viral double-stranded RNAs (dsRNAs). However, growing evidence suggests that PKR can also be activated by endogenously expressed dsRNAs. Here, we capture these dsRNAs by formaldehyde-mediated crosslinking and immunoprecipitation sequencing and find that various noncoding RNAs interact with PKR. Surprisingly, the majority of the PKR-interacting RNA repertoire is occupied by mitochondrial RNAs (mtRNAs). MtRNAs can form intermolecular dsRNAs owing to bidirectional transcription of the mitochondrial genome and regulate PKR and eIF2α phosphorylation to control cell signaling and translation. Moreover, PKR activation by mtRNAs is counteracted by PKR phosphatases, disruption of which causes apoptosis from PKR overactivation even in uninfected cells. Our work unveils dynamic regulation of PKR even without infection and establishes PKR as a sensor for nuclear and mitochondrial signaling cues in regulating cellular metabolism.

Protein kinase R and its cellular regulators in cancer: An active player or a surveillant?

“…In fact, PKR‐associated mtRNAs are most likely to be in a duplex form, as indicated by a nearly equimolar ratio between sense and antisense sequences in PKR fCLIP‐seq reads and by their resistance to RNase T1 that cleaves ssRNA. PKR is mainly localized in the cytoplasm but also detected in the peri‐ and intra‐mitochondrial region, to be activated by mtRNAs upon stress conditions, for example, staurosporine in a study (Kim et al, ). Staurosporine activates PKR for apoptosis, and this activation is due to increasing mtRNA expression, as shown by withdrawal of eIF2α phosphorylation by knockdown of mitochondrial RNA polymerase.…”

Double-Stranded RNA Sensors and Modulators in Innate Immunity

“…Similarly, breakdown of the nuclear membrane during mitosis and consequent exposure of an excess amount of nuclear IR-Alus were also proposed to activate PKR (82). Additional sources of endogenous ligands for PKR include cellular small nucleolar RNAs (snoRNAs) (83) and dsRNAs formed by mitochondrial sense and antisense transcripts (84), although mechanistic details of how these RNAs access cytosolic PKR remain unclear. Intriguingly, RNAs with short stem loops were also shown to activate PKR in a 5 ′ ppp-dependent manner (85).…”

SIDT2 RNA transporter promotes lung and gastrointestinal tumor development

“…Specifically, the type I IFN response to cytoplasmic dsRNA is mainly orchestrated by the RIG-I-like receptors (RLRs), RIG-I and MDA-5 32,33 . RIG-I specifically recognizes short dsRNA and ssRNA with 5' triphosphate ends 34,35 -a common feature of viral RNAs -and MDA-5 is critical for the detection of long dsRNAs (>1000 bp) [36][37][38] 46 . These RNA species may therefore be more likely to accumulate in the absence of SIDT2.…”